BMRB Entry 4781
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR4781
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Title: NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform PubMed: 10860728
Deposition date: 2000-07-10 Original release date: 2002-04-04
Authors: Amarasinghe, Gaya; De Guzman, Roberto; Turner, Ryan; Summers, Michael
Citation: Amarasinghe, Gaya; De Guzman, Roberto; Turner, Ryan; Summers, Michael. "NMR Structure of Stem-loop SL2 of the HIV-1 Psi RNA Packaging Signal Reveals a Novel A-U-A Base-triple Platform" J. Mol. Biol. 299, 145-156 (2000).
Assembly members:
HIV-1 SL2 stem loop, polymer, 19 residues, 6371 Da.
NCp7 protein, polymer, 55 residues, 6372 Da.
Natural source: Common Name: HIV-1 Taxonomy ID: not available Superkingdom: Viruses Kingdom: not available Genus/species: Lentivirus Human Immunodeficiency virus
Experimental source: Production method: enzymatic semisynthesis
Entity Sequences (FASTA):
HIV-1 SL2 stem loop: GGCGACUGGUGAGUACGCC
NCp7 protein: MQKGNFRNQRKTVKCFNCGK
EGHIAKNCRAPRKKGCWKCG
KEGHQMKDCTERQAN
| Data type | Count |
| 13C chemical shifts | 272 |
| 15N chemical shifts | 58 |
| 1H chemical shifts | 456 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | SL2 RNA | 1 |
| 2 | NCp7 | 2 |
Entities:
Entity 1, SL2 RNA 19 residues - 6371 Da.
| 1 | G | G | C | G | A | C | U | G | G | U | ||||
| 2 | G | A | G | U | A | C | G | C | C |
Entity 2, NCp7 55 residues - 6372 Da.
| 1 | MET | GLN | LYS | GLY | ASN | PHE | ARG | ASN | GLN | ARG | ||||
| 2 | LYS | THR | VAL | LYS | CYS | PHE | ASN | CYS | GLY | LYS | ||||
| 3 | GLU | GLY | HIS | ILE | ALA | LYS | ASN | CYS | ARG | ALA | ||||
| 4 | PRO | ARG | LYS | LYS | GLY | CYS | TRP | LYS | CYS | GLY | ||||
| 5 | LYS | GLU | GLY | HIS | GLN | MET | LYS | ASP | CYS | THR | ||||
| 6 | GLU | ARG | GLN | ALA | ASN |
Samples:
sample_1: HIV-1 SL2 stem loop0.6 – 1.2 mM; NCp7 protein0.6 – 1.2 mM
sample_2: HIV-1 SL2 stem loop, [U-13C], 0.8 mM; NCp7 protein, [U-13C; U-15N], 0.8 mM
sample_3: HIV-1 SL2 stem loop0.8 – 1.2 mM; NCp7 protein, [U-15N], 0.8 – 1.2 mM
Ex-cond-1: pH*: 6.5; temperature: 298 K
Ex-cond-2: pH*: 6.5; temperature: 278 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D NOESY | not available | not available | not available |
| 2D TOCSY | not available | not available | not available |
| 2D DQF COSY | not available | not available | not available |
| 1H-13C HMQC | not available | not available | not available |
| 1H,1H,13C HMQC-NOESY | not available | not available | not available |
| 1H,1H,13C HCCH-COSY | not available | not available | not available |
| 1H,1H,13C HCCH-TOCSY | not available | not available | not available |
| 1H,1H,15N HSQC-NOESY | not available | not available | not available |
Software:
XWINNMR v2.6 - Data aquisition on from the NMR
NMRPipe v1.0 - Data processing
NMRView v3.0 - Data analysis
DYANA v1.5 - Structure calculation
CNS v1.0 - Structure refinement and energy minimization
NMR spectrometers:
- Bruker Avance DMX 600 MHz
- Bruker Avance DRX 800 MHz
Related Database Links:
| DBJ | BAC02557 BAC77486 BAC77487 BAC77511 BAC77512 |
| EMBL | CAD26937 CAD26939 CAD26945 CAD26946 CAD26947 |
| GenBank | AAA44987 AAA81036 AAB60571 AAC28445 AAD03199 |
| SWISS-PROT | P12493 P12497 P35962 P35963 Q73367 |
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